OBJECTIVES: Heart rate variability (HRV) has been used to assess sympathetic and parasympathetic modulation of heart rate. Chronic stress relates to reduced HRV. Malocclusion has effects on quality of life, which can lead to chronic stress. Therefore, we hypothesized that malocclusion, as chronic stress, may contribute to reduced HRV. The aim of this study was to investigate the relationship between malocclusion and HRV indices in healthy young adults. METHODS: Thirty-seven non-smoking healthy subjects, aged 22 to 25 years, were examined. Malocclusion was defined by Angle classification. HRV indices included root mean square of successive differences, low frequency (LF), high frequency (HF) and ratio of LF to HF. The effects of malocclusion on quality of life and mental health were assessed using self-reported questionnaires, the condition-specific Oral Impacts on Daily Performances index (CS-OIDP) and the Hopkins Symptoms Checklist (HSCL), respectively. RESULTS: Significantly lower score of HF and higher heart rate (HR) level and CS-OIDP score were observed in subjects with malocclusion (n = 17) compared to those in the control subjects (n = 20) ( P <0.05). There was a positive correlation between HR and score of "anxiety" in HSCL ( P <0.05). CONCLUSIONS: The data showed an association between malocclusion and lower HRV. Based on our results, orthodontic treatment might contribute not only to improvement of oral esthetic and functional problems but also to improvement of stress and HRV indices.